ProtocolHowTo < Lab

---+!! How to Create a Protocol

%TOC%

---++ Tips for Design

 You should generally organize a protocol to have sections that are relevant from this list:
   * Supplies (materials, strains, primers)
   * Step-by-step instructions for each step
   * Expected results (quantitative information, graphics, images)
   * Common problems and troubleshooting
   * Spreadsheets for calculations

Include instructions that reference specific reagents (strains, primers, etc.) for performing *positive* and *negative* control reactions. It is very important and can save a great deal of time if you run these reactions to diagnose bad reagents or a general problem with carrying out the protocol versus a problem with applying it in a specific case.

*These protocols are public, so don't post passwords, protected information, or copyrighted material. Use the [[InternalList][internal Barrick Lab web pages]] for that.*

---++ How to Create a New Protocol / Wiki Page

   1 Navigate to the page that will link to your new page.
   1 Edit this page.
      * Add a link using this syntax: <verbatim>[[TopicName][Link Text]]</verbatim>
      * =TopicName= should be a [[TWiki.WikiWord][WikiWord]] that is descriptive of the new topic. Many topics on the Barrick Lab pages begin with certain words indicating how they are categorized, e.g. "Protocol", "Reference", "Internal".
      * =Link Text= will be the text of the hyperlink that appears on the web page.
      * Save your edit.
   1 Now, a red link to your new page should appear when you view this page. 
   1 Click on the red link and you will be taken to the edit window for your new page!

---++ Heading Display Examples
Using the table to contents (=%<nop>TOC%=) is a great way to organize thoughts or sections of the page. There are 6 headings available, signified by between 1 and 6 + symbols. You can make use of the preformatted heading styles even if you do not want items to appear in the table of contents by adding 2 !! symbols after the last +. Styles are as follows:
---+!! Heading 1
---++!! Heading 2
---+++!! Heading 3
---++++!! Heading 4
---+++++!! Heading 5
---++++++!! Heading 6

---++ Lists
Lists come in bulleted and number varieties and indention length is set by multiples of 3 spaces. They can be mixed.
   * This is a single level indented bullet
      1 This is a second level indented numbered list
         A. This is a third level indented lettered list
      A. This second level indented list resumes counting where it left off, even though it changes from numbered to lettered
            i. This Fourth level indented lower case Roman numeral list (note how it inherited an assumed third level indent)
            I. This Fourth level indented upper case Roman numeral list
      a. Again the 2nd level indented list changes formatting.
      * and a final second level indented bulleted list

In the above lists, twiki is doing the counting for you so you need only use "1", "A.", "a.", "I.", and "i." to get A,B,i,IV etc style formatting. This is especially helpful when you want to insert a new clarifying step in the middle of a protocol and not have to renumber all subsequent steps. While "*" and "1" can be used with a multiple of 3 spaces followed by a single space, A,a,I,i require a "." before the space to denote their list involvement.

---++ Icons
Icons are a simple way to help draw attention. Any can be invoked by "name" using:
   * =%<nop>ICON{"help"}%= returns: %ICON{"help"}%
   * =%<nop>ICON{"tip"}%= returns: %ICON{"tip"}%

[[TWiki.TWikiDocGraphics][A list of icons available.]]

While some can be invoked more easily with a shorthand:
   * =%<nop>H%= also returns: %H%
   * =%<nop>T%= also returns: %T%

[[TWiki.TWikiRenderingShortcuts][A list of shorthand rendering codes.]]

---++ How to Add Images

   1 Click the "attach" link at the bottom of your page
   1 Choose your image file:
      * Avoid spaces in the file name. Use underscores instead.
      * Under "Properties" check the box called "Create a link to the attached file."
   1 After you click "Upload file" your image will appear at the bottom of the page after a bullet point.
   1 Now edit the page and move the =<img>= tag to where you want it displayed in the page.

Tips:
   * If you accidentally forget to hide the attachment, you can click on the attach link and then edit the properties of the file you uploaded at any later time. 
   * You can refer to an image that is attached to a different page with this syntax: <verbatim> <img src="%PUBURL%/%WEB%/OtherTopic/image.jpg"> </verbatim>

---++ Further Tips for Editing the Wiki

Try editing a page where you see what you want to do and copying the syntax!! Monkey see, Monkey do.

General resources
   * [[TWiki.TextFormattingRules][TextFormattingRules (Shorthand)]]
   * [[TWiki.TWikiVariables][TWiki Variables]]
   * [[TWiki.TWikiDocGraphics][TWiki Icons]]
   * [[TWiki.TWikiReferenceManual][TWiki Reference Manual]] 

Useful links for editing the Barrick Wiki
   *  [[WebLeftBar][Edit the left side bar menu]] 

Useful links for administering the Barrick Wiki
   * [[WebAdministration][Web Administration]]
   * [[TWiki.TWikiRegistration][Register New TWiki User]] (requires admin)
   * [[TWiki.ChangePassword][Change Password]] | [[TWiki.ResetPassword][Reset Forgotten Password]]
   * [[Main.TWikiUsers][Users]]
This topic: Lab > WebHome > ProtocolList > ProtocolHowTo
Topic revision: r13 - 2023-09-23 - JeffreyBarrick